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- PDB-5keu: Crystal Structure of a Taurine Dioxygenase from Burkholderia xeno... -

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Basic information

Entry
Database: PDB / ID: 5keu
TitleCrystal Structure of a Taurine Dioxygenase from Burkholderia xenovorans
ComponentsTaurine dioxygenase
KeywordsOXIDOREDUCTASE / SSGCID / dioxygenase / Burkholderia xenovorans / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


2-oxoglutarate-dependent dioxygenase activity / metal ion binding / cytoplasm
Similarity search - Function
: / Clavaminate synthase-like / Double-stranded beta-helix / TauD/TfdA-like domain / Taurine catabolism dioxygenase TauD, TfdA family / Taurine dioxygenase TauD-like superfamily / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / Taurine dioxygenase
Similarity search - Component
Biological speciesBurkholderia xenovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of a Taurine Dioxygenase from Burkholderia xenovorans
Authors: Dranow, D.M. / Lorimer, D. / Edwards, T.E.
History
DepositionJun 10, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Taurine dioxygenase
B: Taurine dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,77628
Polymers71,6072
Non-polymers1,16926
Water12,466692
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6290 Å2
ΔGint-29 kcal/mol
Surface area22050 Å2
MethodPISA
2
A: Taurine dioxygenase
B: Taurine dioxygenase
hetero molecules

A: Taurine dioxygenase
B: Taurine dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,55256
Polymers143,2144
Non-polymers2,33952
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area17000 Å2
ΔGint-81 kcal/mol
Surface area39680 Å2
MethodPISA
3
A: Taurine dioxygenase
hetero molecules

A: Taurine dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,42420
Polymers71,6072
Non-polymers81718
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area3360 Å2
ΔGint-29 kcal/mol
Surface area23790 Å2
MethodPISA
4
B: Taurine dioxygenase
hetero molecules

B: Taurine dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,12836
Polymers71,6072
Non-polymers1,52134
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area6120 Å2
ΔGint-41 kcal/mol
Surface area23410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.270, 133.130, 55.440
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-805-

HOH

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Components

#1: Protein Taurine dioxygenase / BuxeA.00024.c


Mass: 35803.484 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia xenovorans (strain LB400) (bacteria)
Strain: LB400 / Gene: Bxe_C0112 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q13IQ2
#2: Chemical...
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 692 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.91 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: BuxeA.00024.c.B1.PS02531 at 10.4 mg/ml, protein mixed 1:1 and incubated with an equal volume JCSG+(a5): 20% (w/v) PEG-3350, 200 mM magnesium formate, and cryoprotected with 20% ethylene glycol in two steps

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 13, 2016 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 69151 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Biso Wilson estimate: 19.69 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.061 / Net I/σ(I): 21.3
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.85-1.90.4583.59199.9
1.9-1.950.3784.541100
1.95-2.010.2716.11199.9
2.01-2.070.2058.07199.9
2.07-2.140.1749.58199.9
2.14-2.210.14511.46199.9
2.21-2.290.13812.33199.9
2.29-2.390.11214.681100
2.39-2.490.09816.821100
2.49-2.620.08119.78199.9
2.62-2.760.06723.511100
2.76-2.930.05428.94199.9
2.93-3.130.04534.1199.9
3.13-3.380.03740.83199.9
3.38-3.70.03345.76199.9
3.7-4.140.02951.29199.8
4.14-4.780.02655.36199.9
4.78-5.850.02652.311100
5.85-8.270.02552.54199.7
8.27-500.02259.99195.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HSX

5hsx


Resolution: 1.85→41.061 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.25
RfactorNum. reflection% reflection
Rfree0.1782 1973 2.85 %
Rwork0.1506 --
obs0.1513 69143 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 95.04 Å2 / Biso mean: 24.0685 Å2 / Biso min: 4.39 Å2
Refinement stepCycle: final / Resolution: 1.85→41.061 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4302 0 84 697 5083
Biso mean--50.8 33.82 -
Num. residues----551
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074574
X-RAY DIFFRACTIONf_angle_d0.9296235
X-RAY DIFFRACTIONf_chiral_restr0.061701
X-RAY DIFFRACTIONf_plane_restr0.007803
X-RAY DIFFRACTIONf_dihedral_angle_d16.1822662
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8499-1.89620.24021290.195347294858100
1.8962-1.94750.21711730.183546884861100
1.9475-2.00480.19651320.167247544886100
2.0048-2.06950.20571480.159447534901100
2.0695-2.14340.19461330.149847314864100
2.1434-2.22930.19761450.149247694914100
2.2293-2.33070.18421490.153147324881100
2.3307-2.45360.18841480.15547744922100
2.4536-2.60730.19081300.154347814911100
2.6073-2.80850.17161520.149247944946100
2.8085-3.09110.19411340.146848424976100
3.0911-3.53820.15821470.140548214968100
3.5382-4.45680.15391280.130149055033100
4.4568-41.07160.15681250.15895097522299
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.15080.511-0.04640.7731-0.25050.71840.0942-0.33820.21450.1832-0.1241-0.1254-0.23050.10380.0170.2501-0.0928-0.03670.16150.00030.185623.857130.21121.7379
21.23790.9617-0.21231.5959-0.38060.3017-0.0205-0.043-0.0265-0.0286-0.0816-0.1694-0.04230.03060.12030.1111-0.0210.01340.13690.03420.144321.230616.590411.0548
30.7750.6369-0.08171.5848-0.48860.36660.0452-0.1249-0.0091-0.0111-0.1433-0.1242-0.04210.07730.06410.1039-0.0396-0.00240.17120.01390.095312.093611.307319.3031
40.77370.4714-0.05151.6288-1.48121.57890.0261-0.1912-0.1395-0.0176-0.2678-0.31570.09370.10690.28960.1486-0.0519-0.00910.21950.04770.195424.045313.462618.9552
52.1390.9222-0.28476.401-2.96394.7936-0.03830.31910.44920.0056-0.134-0.3601-0.46530.20590.12430.1539-0.0099-0.00390.13990.05250.246311.684533.52-4.8512
61.2035-0.6520.69242.1149-0.40141.3580.01280.04660.371-0.0615-0.0596-0.0163-0.146-0.03570.0270.17970.018-0.01120.12280.04730.2365-1.868539.3281-6.703
71.2945-1.95080.85183.9425-1.18780.9967-0.0598-0.01890.03050.21060.07340.393-0.1133-0.1303-0.05520.13160.01430.02380.159-0.00870.1962-10.570226.40414.1513
80.4446-0.04690.25071.54330.11640.36110.0540.0110.0714-0.1132-0.13930.1392-0.0319-0.02380.06350.12830.0528-0.00310.1266-0.00950.1099-4.225515.901-4.6689
91.6736-0.15480.65912.01640.09761.02450.0831-0.10370.14780.0593-0.1240.049-0.0279-0.07930.07320.1320.02330.00910.10340.00820.115-2.713726.9260.023
105.0178-2.5945-2.26248.13335.80978.5321-0.0466-0.40590.16990.0231-0.06171.0219-0.7256-0.51470.10360.35910.0654-0.03360.28280.04190.4347-19.386722.298-4.1274
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 90 )A10 - 90
2X-RAY DIFFRACTION2chain 'A' and (resid 91 through 141 )A91 - 141
3X-RAY DIFFRACTION3chain 'A' and (resid 142 through 273 )A142 - 273
4X-RAY DIFFRACTION4chain 'A' and (resid 274 through 315 )A274 - 315
5X-RAY DIFFRACTION5chain 'B' and (resid 10 through 26 )B10 - 26
6X-RAY DIFFRACTION6chain 'B' and (resid 27 through 80 )B27 - 80
7X-RAY DIFFRACTION7chain 'B' and (resid 81 through 118 )B81 - 118
8X-RAY DIFFRACTION8chain 'B' and (resid 119 through 240 )B119 - 240
9X-RAY DIFFRACTION9chain 'B' and (resid 241 through 298 )B241 - 298
10X-RAY DIFFRACTION10chain 'B' and (resid 299 through 315 )B299 - 315

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